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Roja B, Saranya S, Chellapandi P. Discovery of novel virulence mechanisms in Clostridium botulinum type A3 using genome-wide analysis. Gene 2023; 869:147402. [PMID: 36972858 DOI: 10.1016/j.gene.2023.147402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/01/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
OBJECTIVE Clostridium botulinum type A is a neurotoxin-producing, spore-forming anaerobic bacterium that causes botulism in humans. The evolutionary genomic context of this organism is not yet known to understand its molecular virulence mechanisms in the human intestinal tract. Hence, this study aimed to investigate the mechanisms underlying virulence and pathogenesis by comparing the genomic contexts across species, serotypes, and subtypes. METHODS A comparative genomic approach was used to analyze evolutionary genomic relationships, intergenomic distances, syntenic blocks, replication origins, and gene abundance with phylogenomic neighbors. RESULTS Type A strains have shown genomic proximity to group I strains with distinct accessory genes and vary even within subtypes. Phylogenomic data showed that type C and D strains were distantly related to a group I and group II strains. Synthetic plots indicated that orthologous genes might have evolved from Clostridial ancestry to subtype A3 strains, whereas syntonic out-paralogs might have emerged between subtypes A3 and A1 through α-events. Gene abundance analysis revealed the key roles of genes involved in biofilm formation, cell-cell communication, human diseases, and drug resistance compared to the pathogenic Clostridia. Moreover, we identified 43 unique genes in the type A3 genome, of which 29 were involved in the pathophysiological processes and other genes contributed to amino acid metabolism. The C. botulinum type A3 genome contains 14 new virulence proteins that can provide the ability to confer antibiotic resistance, virulence exertion and adherence to host cells, the host immune system, and mobility of extrachromosomal genetic elements. CONCLUSION The results of our study provide insight into the understanding of new virulence mechanisms to discover new therapeutics for the treatment of human diseases caused by type A3 strains.
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Affiliation(s)
- B Roja
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli-620024, Tamil Nadu, India
| | - S Saranya
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli-620024, Tamil Nadu, India
| | - P Chellapandi
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli-620024, Tamil Nadu, India.
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2
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Amin AB, Zhang L, Zhang J, Mao S. Metagenomic and Metabolomic Insights Into the Mechanism Underlying the Disparity in Milk Yield of Holstein Cows. Front Microbiol 2022; 13:844968. [PMID: 35668764 PMCID: PMC9163737 DOI: 10.3389/fmicb.2022.844968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/02/2022] [Indexed: 01/12/2023] Open
Abstract
This study was conducted to investigate the metabolic mechanism underlying the disparity in the milk yield of Holstein cows. Eighteen lactating Holstein cows in their second parity and 56 (±14.81 SD) days in milking (DIM) were selected from 94 cows. Based on the milk yield of the cows, they were divided into two groups of nine cows each, the high milk yield group (HP) (44.57 ± 2.11 kg/day) and the low milk yield group (LP) (26.71 ± 0.70 kg/day). The experimental cows were fed the same diet and kept under the same management system for more than 60 days. Rumen metagenomics revealed that two Archaea genera, one Bacteria genus, eight Eukaryota genera, and two Virus genera differ between the HP and LP groups. The analysis of metabolites in the rumen fluid, milk, and serum showed that several metabolites differed between the HP and LP groups. Correlation analysis between the predominant microbiota and milk yield-associated metabolites (MP-metabolites) revealed that four Bacteria and two Eukaryota genera have a positive relationship with MP-metabolites. Pathway enrichment analysis of the differential metabolites revealed that five pathways were enriched in all the samples (two pathways in the milk, two pathways in the serum, and one pathway in the rumen fluid). Further investigation revealed that the low milk yield observed in the LP group might be due to an upregulation in dopamine levels in the rumen fluid and milk, which could inhibit the release of prolactin or suppress the action of oxytocin in the udder resulting in reduced milk yield. On the other hand, the high milk yield in the HP group is attributed to an upregulation in citrulline, and N-acetylornithine, which could be used as substrates for energy metabolism in the citric acid cycle and ultimately gluconeogenesis.
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Affiliation(s)
- Abdulmumini B Amin
- Centre for Ruminant Nutrition and Feed Engineering Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,Laboratory for Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Centre for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,Department of Animal Science, Federal University Dutse, Dutse, Nigeria
| | - Lei Zhang
- Centre for Ruminant Nutrition and Feed Engineering Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,Laboratory for Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Centre for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - JiYou Zhang
- Centre for Ruminant Nutrition and Feed Engineering Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,Laboratory for Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Centre for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shengyong Mao
- Centre for Ruminant Nutrition and Feed Engineering Research, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.,Laboratory for Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Centre for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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3
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Comparative genomic analysis of hyper-ammonia producing Acetoanaerobium sticklandii DSM 519 with purinolytic Gottschalkia acidurici 9a and pathogenic Peptoclostridium difficile 630. Genomics 2021; 113:4196-4205. [PMID: 34780936 DOI: 10.1016/j.ygeno.2021.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/18/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
Acetoanaerobium sticklandii DSM519 (CST) is a hype-ammonia producing non-pathogenic anaerobe that can use amino acids as important carbon and energy sources through the Stickland reactions. Biochemical aspects of this organism have been extensively studied, but systematic studies addressing its metabolic discrepancy remain scant. In this perspective, we have intensively analyzed its genomic and metabolic characteristics to comprehend the evolutionary conservation of amino acid catabolism by a comparative genomic approach. The whole-genome data indicated that CST has shown a phylogenomic similarity with hyper-ammonia producing, purinolytic, and proteolytic pathogenic Clostridia. CST has shown to common genomic context sharing across the purinolytic Gottschalkia acidurici 9a and pathogenic Peptoclostridium difficile 630. Genome syntenic analysis described that syntenic orthologs might be originated from the recent ancestor at a slow evolution rate and syntenic-out paralogs evolved from either CDF or CAC via α-event and β-event. Collinearity of either gene orders or gene families was adjusted with syntenic out-paralogs across these genomes. The genome-wide metabolic analysis predicted 11 unique putative metabolic subsystems from the CST genome for amino acid catabolism and hydrogen production. The in silico analysis of our study revealed that a characteristic system for amino acid catabolism-directed biofuel synthesis might have slowly evolved and established as a core genomic content of CST.
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Youngblut ND, Reischer GH, Dauser S, Maisch S, Walzer C, Stalder G, Farnleitner AH, Ley RE. Vertebrate host phylogeny influences gut archaeal diversity. Nat Microbiol 2021; 6:1443-1454. [PMID: 34702978 PMCID: PMC8556154 DOI: 10.1038/s41564-021-00980-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 09/16/2021] [Indexed: 01/04/2023]
Abstract
Commonly used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut. As a result, several questions regarding the archaeal component of the gut microbiota remain, including which Archaea are host-associated, the specificities of such associations and the major factors influencing archaeal diversity. Using 16S rRNA gene amplicon sequencing with primers that specifically target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected from 110 vertebrate species that span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia and Actinopterygii), of which the majority were wild. We provide evidence for previously undescribed Archaea-host associations, including Bathyarchaeia and Methanothermobacter, the latter of which was prevalent among Aves and relatively abundant in species with higher body temperatures, although this association could not be decoupled from host phylogeny. Host phylogeny explained archaeal diversity more strongly than diet, while specific taxa were associated with both factors, and cophylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last common ancestors of mammals and all host species. Further analysis indicated that Archaea-Bacteria interactions have a limited effect on archaeal diversity. These findings expand our current understanding of Archaea-vertebrate associations.
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Affiliation(s)
- Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.
| | - Georg H Reischer
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Vienna, Austria.,ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Silke Dauser
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sophie Maisch
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Chris Walzer
- Wildlife Conservation Society, Bronx, NY, USA.,Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Gabrielle Stalder
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Andreas H Farnleitner
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Vienna, Austria.,ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria.,Research Division Water Quality and Health, Karl Landsteiner University for Health Sciences, Krems an der Donau, Austria
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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Methanothermobacter thermautotrophicus strain ΔH as a potential microorganism for bioconversion of CO2 to methane. J CO2 UTIL 2020. [DOI: 10.1016/j.jcou.2020.101210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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6
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Prathiviraj R, Chellapandi P. Comparative genomic analysis reveals starvation survival systems in Methanothermobacter thermautotrophicus ΔH. Anaerobe 2020; 64:102216. [PMID: 32504807 DOI: 10.1016/j.anaerobe.2020.102216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 05/07/2020] [Accepted: 05/18/2020] [Indexed: 12/26/2022]
Abstract
Methanothermobacter thermautotrophicus ΔH (MTH) is a thermophilic hydrogenotrophic methanogenic archaeon capable of reducing CO2 with H2 to produce methane gas. It is the potential candidate in the biomethanation of CO2 and CO in anaerobic reactors and biogas upgrading process. However, systematic studies addressing its genome conservation and function remain scant in this genome. In this study, we have evaluated its evolutionary resemblance and metabolic discrepancy, particularly in starvation survival systems by comparing the genomic contexts with Methanothermobacter marburgensis str. Marburg (MMG) and Methanobacterium formicicum DSM 1535 (MFO). The phylogenomic analysis of this study indicated that there was a strong phylogenomic signal among MTH, MMG, and MFO in the whole-genome tree. DNA replication machinery was conserved in the MTH genome and might have evolved at different evolution rates. Genome synteny analysis observed collinearity of either gene orders or gene families has to be maintained with syntenic blocks located in the syntenic out-paralogs. A genome-wide metabolic analysis identified some unique putative metabolic subsystems in MTH, which are proposed to determine its growth characteristics in diverse environments. MTH genome comprised of 93 unique genes-coding for starvation survival and stress-response proteins. These proteins confer its adaptation to nutritional deprivation and other abiotic stresses. MTH has a typical system to withstand its growth and cell viability during stable operation and recovery after prolonged starvation. Thus, the present work will provide an insight to improve the genome refinement and metabolic reconstruction in parallel to other closely related species.
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Affiliation(s)
- R Prathiviraj
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India.
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M B, P C. Comparative analysis of differential proteome-wide protein-protein interaction network of Methanobrevibacter ruminantium M1. Biochem Biophys Rep 2019; 20:100698. [PMID: 31763465 PMCID: PMC6859225 DOI: 10.1016/j.bbrep.2019.100698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 11/22/2022] Open
Abstract
A proteome-wide protein-protein interaction (PPI) network of Methanobrevibacter ruminantium M1 (MRU), a predominant rumen methanogen, was constructed from its metabolic genes using a gene neighborhood algorithm and then compared with closely related rumen methanogens Using proteome-wide PPI approach, we constructed network encompassed 2194 edges and 637 nodes interacting with 634 genes. Network quality and robustness of functional modules were assessed with gene ontology terms. A structure-function-metabolism mapping for each protein has been carried out with efforts to extract experimental PPI concomitant information from the literature. The results of our study revealed that some topological properties of its network were robust for sharing homologous protein interactions across heterotrophic and hydrogenotrophic methanogens. MRU proteome has shown to establish many PPI sub-networks for associated metabolic subsystems required to survive in the rumen environment. MRU genome found to share interacting proteins from its PPI network involved in specific metabolic subsystems distinct to heterotrophic and hydrogenotrophic methanogens. Across these proteomes, the interacting proteins from differential PPI networks were shared in common for the biosynthesis of amino acids, nucleosides, and nucleotides and energy metabolism in which more fractions of protein pairs shared with Methanosarcina acetivorans. Our comparative study expedites our knowledge to understand a complex proteome network associated with typical metabolic subsystems of MRU and to improve its genome-scale reconstruction in the future.
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Affiliation(s)
| | - Chellapandi P
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620 024, Tamil Nadu, India
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8
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Prathiviraj R, Berchmans S, Chellapandi P. Analysis of modularity in proteome-wide protein interaction networks of Methanothermobacter thermautotrophicus strain ΔH and metal-loving bacteria. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42485-019-00019-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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9
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Cheng Q, Huang Y, Nengzi L, Zhang J. Performance and microbial community profiles in pilot-scale biofilter for the simultaneous removal of ammonia, iron and manganese at different manganese concentrations. Bioprocess Biosyst Eng 2019; 42:741-752. [PMID: 30783765 DOI: 10.1007/s00449-019-02077-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 01/17/2019] [Indexed: 11/30/2022]
Abstract
To accelerate extensive application of biological manganese removal technology, a pilot-scale biofilter for ammonia, iron and manganese removal was constructed to investigate the removal performance and microbial community profiles at different manganese concentrations. When manganese in influent increased from 1 to 10 mg/L, the pollutants were completely removed. Ammonia and iron was slightly changed along the filter depth, while manganese obviously increased. In 0 m of the filter depth, the abundance of Gallionella (iron oxidizing bacteria, IOB) increased, while Crenothrix (IOB) decreased. The abundance of Gallionella (manganese oxidizing bacteria, MnOB) in 0.4 and 0.8 m increased to 16.82% and 12.37%, respectively; and Crenothrix (MnOB) in 0.8 m increased to 19.95%, but decreased to 25.08% in 0.4 m. The abundance of ammonia oxidizing bacteria (AOB, Nitrosococcus) decreased in 0.4 and 0.8 m. The biofilter presented a high ability to remove manganese, and had a broad application prospect.
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Affiliation(s)
- Qingfeng Cheng
- College of Resources and Environment, Chengdu University of Information Technology, Chengdu, 610225, People's Republic of China.
| | - Yang Huang
- College of Resources and Environment, Chengdu University of Information Technology, Chengdu, 610225, People's Republic of China
| | - Lichao Nengzi
- College of Resources and Environment, Xichang University, Xichang, 615000, People's Republic of China
| | - Jie Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090, People's Republic of China
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Cheng Q, Huang Y, Nengzi L, Liu J, Zhang J. Performance and microbial community profiles in pilot-scale biofilter for ammonia, iron and manganese removal at different dissolved oxygen concentrations. World J Microbiol Biotechnol 2019; 35:43. [DOI: 10.1007/s11274-019-2617-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/09/2019] [Indexed: 10/27/2022]
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11
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Functional annotation of operome from Methanothermobacter thermautotrophicus ΔH: An insight to metabolic gap filling. Int J Biol Macromol 2018; 123:350-362. [PMID: 30445075 DOI: 10.1016/j.ijbiomac.2018.11.100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/10/2018] [Accepted: 11/12/2018] [Indexed: 12/16/2022]
Abstract
Methanothermobacter thermautotrophicus ΔH (MTH) is a potential methanogen known to reduce CO2 with H2 for producing methane biofuel in thermophilic digesters. The genome of this organism contains ~50.5% conserved hypothetical proteins (HPs; operome) whose function is still not determined precisely. Here, we employed a combined bioinformatics approach to annotate a precise function to HPs and categorize them as enzymes, binding proteins, and transport proteins. Results of our study show that 315 (35.6%) HPs have exhibited well-defined functions contributing imperative roles in diverse cellular metabolism. Some of them are responsible for stress-response mechanisms and cell cycle, membrane transport, and regulatory processes. The genome-neighborhood analysis found five important gene clusters (dsr, ehb, kaiC, cmr, and gas) involving in the energetic metabolism and defense systems. MTH operome contains 223 enzymes with 15 metabolic subsystems, 15 cell cycle proteins, 17 transcriptional regulators and 33 binding proteins. Functional annotation of its operome is thus more fundamental to a profound understanding of the molecular and cellular machinery at systems-level.
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Chellapandi P, Bharathi M, Sangavai C, Prathiviraj R. Methanobacterium formicicum as a target rumen methanogen for the development of new methane mitigation interventions: A review. Vet Anim Sci 2018; 6:86-94. [PMID: 32734058 PMCID: PMC7386643 DOI: 10.1016/j.vas.2018.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 08/29/2018] [Accepted: 09/12/2018] [Indexed: 12/18/2022] Open
Abstract
Methanobacterium formicicum (Methanobacteriaceae family) is an endosymbiotic methanogenic Archaean found in the digestive tracts of ruminants and elsewhere. It has been significantly implicated in global CH4 emission during enteric fermentation processes. In this review, we discuss current genomic and metabolic aspects of this microorganism for the purpose of the discovery of novel veterinary therapeutics. This microorganism encompasses a typical H2 scavenging system, which facilitates a metabolic symbiosis across the H2 producing cellulolytic bacteria and fumarate reducing bacteria. To date, five genome-scale metabolic models (iAF692, iMG746, iMB745, iVS941 and iMM518) have been developed. These metabolic reconstructions revealed the cellular and metabolic behaviors of methanogenic archaea. The characteristics of its symbiotic behavior and metabolic crosstalk with competitive rumen anaerobes support understanding of the physiological function and metabolic fate of shared metabolites in the rumen ecosystem. Thus, systems biological characterization of this microorganism may provide a new insight to realize its metabolic significance for the development of a healthy microbiota in ruminants. An in-depth knowledge of this microorganism may allow us to ensure a long term sustainability of ruminant-based agriculture.
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Affiliation(s)
- P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024, India
| | - M Bharathi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024, India
| | - C Sangavai
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024, India
| | - R Prathiviraj
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024, India
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Luo H, Quan CL, Peng C, Gao F. Recent development of Ori-Finder system and DoriC database for microbial replication origins. Brief Bioinform 2018; 20:1114-1124. [DOI: 10.1093/bib/bbx174] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Indexed: 01/28/2023] Open
Abstract
Abstract
DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Furthermore, the Web servers of Ori-Finder and Ori-Finder 2 have been developed to predict replication origins in both bacterial and archaeal genomes based on the Z-curve method, and the replication origins with manual curation have been collected into an online database, DoriC. Ori-Finder system and DoriC database are currently used in the research field of DNA replication origins in prokaryotes, including: (i) identification of oriC regions in bacterial and archaeal genomes; (ii) discovery and analysis of the conserved sequences within oriC regions; and (iii) strand-biased analysis of bacterial genomes.
Up to now, more and more predicted results by Ori-Finder system were supported by subsequent experiments, and Ori-Finder system has been used to identify the replication origins in > 100 newly sequenced prokaryotes in their genome reports. In addition, the data in DoriC database have been widely used in the large-scale analyses of replication origins and strand bias in prokaryotic genomes. Here, we review the development of Ori-Finder system and DoriC database as well as their applications. Some future directions and aspects for extending the application of Ori-Finder and DoriC are also presented.
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Cheng Q, Nengzi L, Bao L, Huang Y, Liu S, Cheng X, Li B, Zhang J. Distribution and genetic diversity of microbial populations in the pilot-scale biofilter for simultaneous removal of ammonia, iron and manganese from real groundwater. CHEMOSPHERE 2017; 182:450-457. [PMID: 28521159 DOI: 10.1016/j.chemosphere.2017.05.075] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 03/27/2017] [Accepted: 05/12/2017] [Indexed: 06/07/2023]
Abstract
A pilot-scale biofilter treating real groundwater was developed in this study, which showed that ammonia, iron and manganese were mainly removed at 0.4, 0.4 and 0.8 m of the filter bed, respectively, and the corresponding removal efficiencies were 90.82%, 95.48% and 95.90% in steady phase, respectively. The variation of microbial populations in the biofilter during start-up process was also investigated using high-throughput pyrosequencing (HTP). Results indicated that the main functional microbes for ammonia, iron and manganese removal were Nitrosomonas, Crenothrix and Crenothrix, respectively, which was mainly distributed at 0.8, 0, and 0.8 m of the filter bed with a corresponding abundance of 8.7%, 28.12% and 11.33% in steady phase, respectively. Kinds of other bacteria which may be related to methane, hydrogen sulfide and organic matter removal, were also found. In addition, small part of archaea was also detected, such as Candidatus Nitrososphaera, which plays a role in nitritation.
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Affiliation(s)
- Qingfeng Cheng
- College of Resources and Environment, Chengdu University of Information Technology, Chengdu 610225, PR China; Key Laboratory for Yellow River and Huaihe River Water Environment and Pollution Control Ministry of Education, Henan Key Laboratory of Environmental Pollution Control, School of Environment, Henan Normal University, Xinxiang 453007, PR China; State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China.
| | - Lichao Nengzi
- College of Resources and Environment, Chengdu University of Information Technology, Chengdu 610225, PR China
| | - Linlin Bao
- Key Laboratory for Yellow River and Huaihe River Water Environment and Pollution Control Ministry of Education, Henan Key Laboratory of Environmental Pollution Control, School of Environment, Henan Normal University, Xinxiang 453007, PR China
| | - Yang Huang
- College of Resources and Environment, Chengdu University of Information Technology, Chengdu 610225, PR China
| | - Shengyu Liu
- College of Resources and Environment, Chengdu University of Information Technology, Chengdu 610225, PR China
| | - Xiuwen Cheng
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lake, Chinese Academy of Sciences, Xinning Road 18, Chengxi District, Xining 810008, PR China; Key Laboratory of Western China's Environmental Systems (Ministry of Education) and Key Laboratory for Environmental Pollution Prediction and Control, Gansu Province, College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, PR China
| | - Bo Li
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lake, Chinese Academy of Sciences, Xinning Road 18, Chengxi District, Xining 810008, PR China
| | - Jie Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
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